Two distinct classes of acetylcholinesterase exist in near equal amounts in the electric organ of Torpedo californica. A globular 5.6 S form is a dimer which possesses a hydrophobic region. The second form is present as elongated species that sediment at 17 and 13 S and contain structural subunits disulfide-linked to the catalytic subunits. Removal of the structural subunits by mild proteolysis yields a tetramer of catalytic subunits which sediments at 11 S. To compare the primary structures of the catalytic subunits of the 5.6 S and 11 S forms of acetylcholinesterase, amino acid sequences from the active sites and from the amino-terminal regions have been elucidated. Active site serines were labeled with [3H]isopropyl fluorophosphate. After digestion with trypsin, the resultant peptides were resolved by elution from a size-exclusion column followed by reverse-phase high performance liquid chromatography. Each active site tryptic peptide contained 24 residues and identical sequences were found in this peptide for the 5.6 S and 11 S forms of the enzyme. The sequence flanking the active site serine revealed extensive homology with the published sequence of human serum cholinesterase as well as a lesser degree of homology with other known serine proteases and esterases. The sequences of the amino-terminal region also appear to be identical for both enzyme forms although we note variation in the ratio of Glu and Gln at position 5. The amino-terminal sequence exhibits only partial homology with the published sequence of human serum cholinesterase.